'We are sorry,' Secretary of State Hillary Clinton said about a December attack near the Afghanistan border that killed 24 Pakistani soldiers. That sticking point resolved, a key supply route will reopen, but US-Pakistan ties are weaker now.

Oil tankers, which were used to transport NATO fuel supplies to Afghanistan, are parked, in Karachi, Pakistan, Monday. The Obama administration said Tuesday that Pakistan was reopening its supply lines into Afghanistan, after the US belatedly issued an apology for the November killing of 24 Pakistani troops in a NATO airstrike.

Washington — The United States relented and formally apologized to Pakistan Tuesday for a border incident seven months ago in which 24 Pakistani soldiers died – paving the way for a reopening of critical supply routes for the war in Afghanistan.

Secretary of State Hillary Rodham Clinton issued a carefully worded statement Tuesday morning that was direct in its apology for the December attack by US helicopters on a Pakistani border outpost, and effusive in its praise of Pakistani leaders and their cooperation with the US.

“We are sorry for the losses suffered by the Pakistani military,” Secretary Clinton said, using the S-word that President Obama had until now refused to use over the incident, as Pakistan had demanded. Before Tuesday, the US had gone only so far as to “regret” the loss of life.

Clinton went on to say that “we are committed to working closely with Pakistan and Afghanistan to prevent this from ever happening again,” before concluding with “our deep appreciation to the Government and the people of Pakistan for their many sacrifices and their critical contribution to the ongoing fight against terrorism and extremism.”

The US apology resolved one of the touchiest disputes between the two countries in what has lately been a testy relationship. But it remains to be seen if the new tone signaled in Clinton’s statement carries over into real improvement in relations.

Some Pakistan analysts were quick to warn that the apology and resulting reopening of Pakistan’s border to NATO supplies into Afghanistan would of themselves do little to improve relations or prospects for security in Afghanistan.

“Merely re-opening the supply routes will not help the US achieve its objectives in Afghanistan because it does not address the fundamental problem of continuing Pakistani support for the Taliban and Haqqani network that are killing US and coalition forces on a daily basis in Afghanistan,” says Lisa Curtis, a South Asia expert at the Heritage Foundation in Washington. “Pakistan has never explained – let alone apologized – for its lack of action against the enemies of the US that find sanctuary on its soil,” she says.

Pakistan immediately closed its borders to the transport of NATO supplies into Afghanistan after the Nov. 26 border attack, costing the US and its NATO allies hundreds of millions of dollars in higher transport outlays for more expensive routes and transport methods.

Pentagon officials estimate that the Pakistan land routes into Afghanistan carried about half of all supplies for the Afghan war effort, at about one-tenth the cost of air transport. Defense Secretary Leon Panetta said in congressional testimony in June that using costlier routes (the so-called northern route through Russia and Central Asian countries to Europe) and relying more on air transport was costing the US and its partners in Afghanistan $100 million a month.

Yet Mr. Obama – who had already angered the Pakistanis by stepping up drone strikes against Al Qaeda and Taliban safe havens inside Pakistan, and especially over the successful raid on Osama bin Laden’s compound – refused to apologize for the outpost attack after an investigation revealed joint responsibility for the incident. The US military determined that the helicopter strikes came after Pakistani soldiers in the area first fired on US soldiers across the border in Afghanistan.

Both sides had predicted the dispute would be resolved and the borders would reopen to NATO when Pakistani President Asif Ali Zardari met with Obama on the sidelines of NATO’s summit in Chicago in May. But weeks of negotiations had come down to the matter of an apology, and a deal fell through when both sides refused to blink.

Pakistan had also infuriated the White House with its demand that any reopening of the border come at the price of hugely higher transit fees. At one point in negotiations, Pakistan was demanding that an average per-truck cost of $250 for crossing the border jump to $5,000.

But Clinton said in her statement that Pakistan’s foreign minister, Hinna Rabbani Khar, informed her in a Tuesday morning phone call that Pakistan would charge no transit fee “in the larger interest of peace and security in Afghanistan and the region.”

Clinton also said in her statement that by charging no transit fee, Pakistan “will also help the United States and [international forces in Afghanistan] conduct the planned drawdown at a much lower cost.”

In a separate statement Tuesday, the Pakistani ambassador to Washington, Sherry Rehman, said, “I am glad that this breakthrough is not part of any transaction. We are playing our role as responsible global partner in stabilizing the region.”

Ambassador Rehman added that she hoped the border transport accord would mean that “bilateral ties can move to a better place from here.”

But Ms. Curtis of Heritage says better ties are unlikely because the US and Pakistan will continue to have conflicting goals in Afghanistan.

“The reality is that the US and Pakistan are striving for different outcomes in Afghanistan,” Curtis says. Citing Clinton’s statement in which she calls the restoration of the supply routes a “tangible demonstration of Pakistan’s support for a secure, peaceful, and prosperous Afghanistan and our shared objectives in the region,” Curtis says, “This is simply not true.”

“The tensions between the US and Pakistan will persist," Curtis says, "... until Pakistan aligns its goals more closely with those of the US and NATO in Afghanistan and confronts the Taliban and Haqqani networks inside Pakistan.”